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bioinfo-biols / CIRI-cookbook

Document for CIRI-series software
https://ciri-cookbook.readthedocs.io/en/latest/index.html
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Discussion of inner distance in paired end to ciri2 result #5

Closed gumingmu closed 2 years ago

gumingmu commented 3 years ago

I know CIRI2 will filter reads by PEM signals. But i am confused about if the inner distance of ciricular RNA reads is low, will CIRI2 filter this reads by PEM signals.

Kevinzjy commented 3 years ago

Hi @gumingmu, are you talking about situations where the fragment size is relatively small so distance between read1 and read2 is very small?

As you mentioned, CIRI2 only use PEM signals to filter false positives, which means that if a back-splicing event is detected in read1, read2 must align inside the back-splicing junction. Otherwise, the read pair will be discarded. So as long as the read1 and read2 have correct alignment pattern, their distance won't affect the PEM filter step.